The invention relates to improved bacteria, particularly Escherichia coli (E. coli) bacteria capable of high transformation efficiencies, methods for producing improved bacterial strains capable of high transformation efficiencies, and methods for obtaining high transformation efficiencies with bacteria, particularly E. coli bacteria. Specifically, it relates to methods of producing and using bacteria, particularly E. coli bacteria that contain Fxe2x80x2 episome genetic material and are capable of exhibiting enhanced transformation efficiencies.
High efficiency chemically competent E. coli bacteria (bacterial cells that can be transformed with DNA) are used extensively in the generation of cDNA libraries and the cloning of samples containing small amounts of target sequences. The ability to generate representative cDNA libraries, one in which each mRNA species present in the subject cell is represented in the library, relies on many factors. One of the major factors determining the quality of a cDNA library is the number of clones represented in the library. Using competent bacteria having a high transformation efficiency increases the probability of obtaining rare, under-represented clones in plasmid libraries. Also, when cloning samples containing small amounts of target DNA or cloning the DNA products of complex DNA manipulations such as the DNA products of single or multiple blunt ended ligations, the use of high efficiency bacteria is essential.
Early attempts to achieve transformation of E. coli were unsuccessful and it was generally believed that E. coli was refractory to transformation. However, Mandel and Higa (J. Mol. Bio. 53: 159-162 (1970)) found that treatment with CaCl2 allowed E. coli bacteria to take up DNA from bacteriophage xcex. In 1972, Cohen et al. showed CaCl2-treated E. coli bacteria were effective recipients for plasmid DNA (Cohen et al., Proc. Natl. Acad. Sci., 69: 2110-2114 (1972)). Since transformation of E. coli is an essential step or cornerstone in many cloning experiments, it is desirable that it be as efficient as possible (Lui and Rashidbaigi, BioTechniques 8: 21-25 (1990)). Several groups of workers have examined the factors affecting the efficiency of transformation.
Hanahan (J. Mol. Biol. 166: 557-580 (1983), herein incorporated by reference) examined factors that affect the efficiency of transformation, and devised a set of conditions for optimal efficiency (expressed as transformants per xcexcg of DNA added) applicable to most E. coli K12 strains. Typically, efficiencies of 107 to 109 transformants/xcexcg can be achieved depending on the strain of E. coli and the method used (Liu and Rashidbaigi, BioTechniques 8: 21-25 (1990), herein incorporated by reference).
Many methods for bacterial transformation are based on the observations of Mandel and Higa (J. Mol. Bio. 53: 159-162 (1970)). Apparently, Mandel and Higa""s treatment induces a transient state of xe2x80x9ccompetencexe2x80x9d in the recipient bacteria, during which they are able to take up DNAs derived from a variety of sources. Many variations of this basic technique have since been described, often directed toward optimizing the efficiency of transformation of different bacterial strains by plasmids. Bacteria treated according to the original protocol of Mandel and Higa yield 105-106 transformed colonies/xcexcg of supercoiled plasmid DNA. This efficiency can be enhanced 100- to 1000-fold by using improved strains of E. coli (Kushner, In: Genetic Engineering: Proceedings of the International Symposium on Genetic Engineering, Elsevier, Amsterdam, pp. 17-23 (1978); Norgard et al., Gene 3:279-292 (1978); Hanahan, J. Mol. Biol. 166: 557-580 (1983)) combinations of divalent cations ((Kushner, In: Genetic Engineering: Proceedings of the International Symposium on Genetic Engineering, Elsevier, Amsterdam, pp. 17-23 (1978)) for longer periods of time (Dagert and Ehrlich, Gene 6: 23-28 (1979)) and treating the bacteria with DMSO (Kushner, In: Genetic Engineering: Proceedings of the International Symposium on Genetic Engineering, Elsevier, Amsterdam, pp. 17-23 (1978)), reducing agents, and hexamminecobalt chloride (Hanahan (J. Mol. Biol. 166: 557-580 (1983).
Incubation of E. coli. in solutions that contain multivalent cations is an important step in the transformation of E. coli. A number of multivalent cations are capable of affecting DNA transformation of E. coli. In addition to calcium cations, manganese, magnesium and barium cations can affect DNA transformation of E. coli and the use of manganese or barium cations rather than calcium cations has lead to higher transformation efficiencies with some strains of E. coli (Taketo, Z. Naturforsch Sect. C 30: 520-522 (1975); Taketo, Z. Naturforsch Sect. C 32: 429-433 (1975); Taketo and Kuno, J. Biochem. 75: 895-904 (1975)). A variety of other compounds affect transformation efficiencies. Organic solvents and sulhydryl reagents can also influence transformation efficiencies (Hanahan (J. Mol. Biol. 166: 557-580 (1983); Kushner, In: Genetic Engineering: Proceedings of the International Symposium on Genetic Engineering, Elsevier, Amsterdam, pp. 17-23 (1978); Jessee, J. A. and Bloom, F. R., U.S. Pat. No. 4,981,797 (1991)).
Incubation of E. coli at temperatures around 0xc2x0 C., often on ice, in buffers containing multivalent cations is an important step in the production or generation of competent cells of E. coli. A rapid heat shock or temperature transition after incubation of the E. coli with target DNA further improves transformation efficiencies (Mandel and Higra, (J. Mol. Bio. 53: 159-162 (1970)). Typically, the solutions containing E. coli and target DNA are transferred from 0xc2x0 C. to temperatures between 37 and 42xc2x0 C. for 30 to 120 seconds. The temperature at which E. coli bacteria are grown prior to incubation at 0xc2x0 C. can also affect transformation efficiency. Growing E. coli bacteria at temperatures between 25 and 30xc2x0 C. can improve the transformation efficiency of E. coli bacteria compared with E. coli bacteria grown at 37xc2x0 C. (Jessee, J. A. and Bloom, F. R., U.S. Pat. No. 4,981,797 (1991)). E. coli bacteria that are grown at temperatures between 25 and 30xc2x0 C., in contrast to 37xc2x0 C., may require a heat shock at less than 37 to 42xc2x0 C., or a heat shock of a shorter duration, for optimal results (Jesse and Bloom, U.S. Pat. No. 4,981,797 (1991); Inoue et al. Gene 96:23-28 (1990)).
Transformation efficiency can be affected by the E. coli strain used. The selection of an E. coli strain that is capable of high transformation with the specific competence protocol adopted is an important step in the development of a procedure to produce E. coli bacteria capable of high transformation efficiencies. Different strains can exhibit different transformation efficiencies depending on the competence protocol used. Lui and Rashidbaigi, BioTechniques 8: 21-25 (1990), compared the transformation efficiency of five E. coli strains, HB101, RR1, DH1, SCS1 and JV30 and showed that the transformation efficiencies of these strains varied according to the methodology adopted.
A number of procedures exist for the preparation of competent bacteria and the introduction of DNA into those bacteria. A very simple, moderately efficient transformation procedure for use with E. coli involves re-suspending log-phase bacteria in ice-cold 50 mM calcium chloride at about 1010 bacteria/ml and keeping them ice-cold for about 30 min. Plasmid DNA (0.1 mg) is then added to a small aliquot (0.2 ml) of these now competent bacteria, and the incubation on ice continued for a further 30 min, followed by a heat shock of 2 min at 42xc2x0 C. The bacteria are then usually transferred to nutrient medium and incubated for some time (30 min to 1 hour) to allow phenotypic properties conferred by the plasmid to be expressed, e.g. antibiotic resistance commonly used as a selectable marker for plasmid-containing cells. Protocols for the production of high efficiency competent bacteria have also been described and many of those protocols are based on the protocols described by Hanahan (J. Mol. Biol. 166:557-580 (1983).
The F episome is a genetic element that may exist as a free genetic element or become integrated into the bacterial genome. The presence of the F episome, whether in a free or integrated form, has important consequences for the host bacterium. F-positive bacteria exhibit surface appendages called pilli, which provide attachment sites that facilitate the infection of certain RNA and single-stranded DNA viruses. Many E. coli strains have been constructed to contain an F plasmid in order to facilitate the infection of those strains by single-stranded DNA viruses. E. coli strains engineered for this purpose include: JM101 (Messing, In Recombinant DNA: Proceedings of the Third Cleveland Series on Macromolecules, Elsevier, Amsterdam p 143-153 (1981)); JM105, JM107, JM109 and JM110 (Yanish-Perron et al., Gene 33: 103-119 (1985)); TG1 (Gibson, Ph.D. Thesis, Cambridge University, England (1984)); TG2 (Sambrook et al., In Molecular Cloning: A Laboratory Manual, Cold Spring Harbor p. 4.14 (1989)); XL1-Blue (Bullock et al., BioTechniques 5.4:376-378 (1987)); XS127 and XS101 (Levinson et al., Mol. Appl. Genet. 2:507-517 (1984)); 71/18 (Dente et al., Nucleic Acids Res. 11: 1645-1655 (1983)); KK2186 (Zagursky and Berman, Gene 27:183-191 (1984)); and MV1184 (Viera and Messing, Methods Enzymol. 153: 3-11 (1987)).
Transformation efficiency was not thought to be enhanced by the addition of Fxe2x80x2 episome genetic material. (Hanahan (J. Mol. Biol. 166: 557-580 (1983); Bullock et al. (1987)). Indeed, the addition of a Fxe2x80x2 episome to the E. coli strain AG1 produced an E. coli strain (XL1-Blue) with a reduced transformation efficiency (Bullock et al. (1987)). Contrary to this background, Applicants"" invention involves the use of Fxe2x80x2 genetic material to provide modified E. coli having improved transformation efficiency compared with E. coli without Fxe2x80x2 genetic material.
Another rapid and simple method for introducing genetic material into bacteria is electoporation (Potter, Anal. Biochem. 174: 361-73 (1988)). This technique is based upon the original observation by Zimmerman et al., J. Membr. Biol. 67: 165-82 (1983), that high-voltage electric pulses can induce cell plasma membranes to fuse. Subsequently, it was found that when subjected to electric shock (typically a brief exposure to a voltage gradient of 4000-16000 V/cm), the bacteria take up exogenous DNA from the suspending solution, apparently through holes momentarily created in the plasma membrane. A proportion of these bacteria become stably transformed and can be selected if a suitable marker gene is carried on the transforming DNA transformed (Newman et al., Mol. Gen. Genetics 197: 195-204 (1982)). With E. coli, electroporation has been found to give plasmid transformation efficiencies of 109-1010/xcexcg DNA (Dower et al., Nucleic Acids Res. 16: 6127-6145 (1988)).
Bacterial cells are also susceptible to transformation by liposomes (Old and Primrose, In Principles of Gene Manipulation: An Introduction to Gene Manipulation, Blackwell Science (1995)). A simple transformation system has been developed which makes use of liposomes prepared from cationic lipid (Old and Primrose, (1995)). Small unilamellar (single bilayer) vesicles are produced. DNA in solution spontaneously and efficiently complexes with these liposomes (in contrast to previously employed liposome encapsidation procedures involving non-ionic lipids). The positively-charged liposomes not only complex with DNA, but also bind to bacteria and are efficient in transforming them, probably by fusion with the cells. The use of liposomes as a transformation or transfection system is called lipofection.
The present invention provides novel bacterium, particularly novel E. coli bacterium, capable of high efficiency transformation, whose efficiency of transformation is enhanced by the introduction of Fxe2x80x2 episome genetic material. The invention also concerns methods for the use of novel bacteria, particularly novel E. coli bacteria, whose efficiency of transformation is enhanced by the introduction Fxe2x80x2 episome genetic material. Furthermore, the invention also provides methods for constructing bacteria capable of high efficiency transformation, whose efficiency of transformation is enhanced by the introduction of Fxe2x80x2 episome genetic material. Indeed, the invention may be used for the insertion of exogenous DNA sequences from other E. coli bacteria or other organisms into the novel bacteria of the present invention.
One object of the present invention is to provide a bacterium containing Fxe2x80x2 genetic material capable of an enhanced transformation efficiency. A particular object of the present invention is to provide an E. coli bacterium containing Fxe2x80x2 genetic material capable of an enhanced transformation efficiency.
A further object of the present invention is to provide a process for producing an Enterobacteriacea (especially an E. coli bacterium) containing Fxe2x80x2 genetic material capable of an enhanced transformation efficiency, comprising the following steps: (a) introducing Fxe2x80x2 genetic material into a bacterium; (b) selecting the bacterium containing Fxe2x80x2 genetic material; and (c) recovering the bacterium containing Fxe2x80x2 genetic material.
Another object of the present invention is to provide a process for preparing competent bacteria comprising the following steps: (a) growing a bacterium (especially an E. coli bacterium) containing Fxe2x80x2 genetic material capable of an enhanced transformation efficiency in a growth-conductive medium; and (b) rendering the bacterium competent.
The present invention further concerns a novel bacterium, especially an Enterobacteriacea, and particularly a novel E. coli bacterium capable of high efficiency transformation, whose efficiency of transformation is enhanced by the introduction of Fxe2x80x2 episome genetic material. The present invention also concerns processes for transforming E. coli bacterium containing Fxe2x80x2 genetic material that are capable of enhanced transformation efficiencies.
The present invention pertains to bacteria capable of high efficiency transformation. Such bacteria may be any bacteria whose efficiency of transformation can be enhanced by the introduction of Fxe2x80x2 episome genetic material. Examples of suitable bacteria include bacteria of the Enterobacteriacea, and in particular, bacteria of the genera Escherichia, Salmonella, especially E. coli and Salmonella species. In a preferred embodiment, the bacterium of the present invention may be any E. coli strain capable of high efficiency transformation whose efficiency of transformation is enhanced by the introduction of Fxe2x80x2 episome genetic material. In a further preferred embodiment of the present invention, the bacterium may be any E. coli K strain or derivative or equivalent thereof. As used herein, a xe2x80x9cderivativexe2x80x9d of a bacterium is any bacterium that results from any alteration (or series or alterations), naturally occurring or otherwise, of that bacterium. As used herein, an xe2x80x9cequivalentxe2x80x9d of a bacterium is any bacterium that has a transformation efficiency (as measured by transformants/xcexcg DNA added) that is equivalent to the transformation efficiency of that bacterium. In an even more preferred embodiment, the bacterium of the present invention will preferably be a derivative of E. coli K, such as MM294 (Meselson and Yuan, Nature 217: 1110-1114 (1968), or a derivative or equivalent thereof. In a further even more preferred embodiment, the bacterium of the present invention will be preferably be E. coli DH5xcex1 or a derivative or equivalent thereof, whose efficiency of transformation is enhanced by the introduction of Fxe2x80x2 episome genetic material. In the most preferred embodiment, the bacterium of the present invention will be more preferably be E. coli DH5xcex1, whose efficiency of transformation is enhanced by the introduction of Fxe2x80x2 episome genetic material.
Transformation, in the context of the current invention, is the process by which exogenous DNA is inserted into a bacterium, causing the bacterium to change its genotype and/or phenotype. Such a change in genotype or phenotype may be transient or otherwise. Exogenous DNA is any DNA, whether naturally occurring or otherwise, from any source that is capable of being inserted into any organism. Preferably, exogenous DNA is any DNA, whether naturally occurring or otherwise, from any source that is capable of being inserted into bacteria. More preferably, exogenous DNA is any DNA, whether naturally occurring or otherwise, from any source that is capable of being inserted into DH5xcex1. Even more preferably, exogenous DNA is any DNA, whether naturally occurring or otherwise, from any source that is capable of being inserted into DH5xcex1 bacteria capable of high efficiency transformation, whose efficiency of transformation is enhanced by the introduction of Fxe2x80x2 episome genetic material. Such exogenous DNA includes, without limitation, plasmid DNA and lambda DNA.
The bacteria of the present invention are capable of acting as a recipient for inserted exogenous DNA. In a preferred embodiment, bacteria capable of acting as a recipient for exogenous DNA are prepared by inoculating medium which supports their growth. In a more preferred embodiment, E. coli DH5xcex1 bacteria containing Fxe2x80x2 genetic material capable of an enhanced transformation efficiency are grown at 28xc2x0 C. in SOB media (20 g bacto-trytone, 5 g bacto-yeast extract, 5 g NaCl, per liter, 2.5 mM KCl, 10 mM MgCl2 equilibrated to pH 7.0 with NaOH) media containing additional multivalent cations until the optical density of the solution was 0.3 O.D.550 In an even more preferred embodiment, E. coli DH5xcex1 bacteria containing Fxe2x80x2 genetic material capable of an enhanced transformation efficiency are grown at 28xc2x0 C. in SOB media containing 20 mM magnesium cations until the optical density of the solution is 0.3 O.D.550.
In a preferred embodiment, the bacteria are harvested by centrifugation and resuspended in a solution capable of inducing competence in E. coli. In a more preferred embodiment, E. coli DH5xcex1 bacteria containing Fxe2x80x2 genetic material capable of an enhanced transformation efficiency are harvested by centrifugation at 4xc2x0 C. for 10 minuets at 4,000 rpm and resuspended in FSB (10 mM potassium acetate, 100 mM potassium chloride, 45 mM maganese (II) chloride tetrahydrate, 10 mM calcium chloride dihydrate, 3 mM hexammecolbalt (III) chloride, 10% (volume:volume) glycerol, 5% (weight:volume) sucrose, pH 6.4). In an even more preferred embodiment, the re-suspended bacteria containing Fxe2x80x2 genetic material capable of an enhanced transformation efficiency are subsequently treated with DMSO and can be stored at 70xc2x0 C. for up to 1 year.
In a preferred embodiment, the bacteria are thawed on ice, mixed with exogenous DNA, incubated on ice, and heat treated. In a more preferred embodiment, the frozen E. coli DH5xcex1 bacteria containing Fxe2x80x2 genetic material are thawed on ice for 10 to 15 minuets, mixed with exogenous DNA, incubated on ice for 30 minutes, and heat treated at 42xc2x0 C. for 45 seconds.
In another embodiment of the present invention, the bacteria are treated with high voltage electric pulses in a solution containing exogenous DNA. In a more preferred alternative embodiment of the present invention, the bacteria are E. coli DH5xcex1 containing Fxe2x80x2 genetic material, and are mixed with exogenous DNA and then treated with a brief voltage gradient of 4,000 to 16,000 V/cm.
In a preferred embodiment, high efficiency transformation is preferably 108 or greater transformed bacteria per xcexcg of purified plasmid DNA. High efficiency transformation is more preferably 109 or greater transformed bacteria per xcexcg of purified plasmid DNA.
The present invention also concerns novel E. coli bacteria capable of high efficiency transformation, whose efficiency of transformation is enhanced by the introduction of Fxe2x80x2 episome genetic material. As used herein, such efficiency is said to be xe2x80x9cenhancedxe2x80x9d if the presence of Fxe2x80x2 episome genetic material increases the efficiency of transformation of a bacterium. In the preferred embodiment the efficiency of the present invention is enhanced by a factor of greater than one. In a more preferred embodiment, the transformation efficiency of the present invention is enhanced by 2-4 fold. In a even more preferred embodiment, the transformation efficiency of the present invention is enhanced by greater than 4 fold.
The present invention concerns a novel E. coli bacterium capable of high efficiency transformation, where said transformation alters the bacterium""s genotype and/or transiently alters the bacterium""s phenotype. The genotype of an organism is the genetic constitution of an organism. The phenotype of the organism are the characteristics of an organism.
The present invention concerns novel E. coli bacteria capable of high efficiency transformation, whose efficiency of transformation is enhanced by the introduction of certain Fxe2x80x2 episome genetic material. In a preferred embodiment, the bacteria contains all or part of the Fxe2x80x2 episome genetic material integrated into the E. coli chromosome. In another preferred embodiment, the bacteria contains all or part of the Fxe2x80x2 episome genetic material on a self replicating DNA molecule. In a more preferred embodiment, all or part of the Fxe2x80x2 episome genetic material is genetically linked to a selectable marker. In an even more preferred embodiment, the Fxe2x80x2 episome genetic material is linked to an selectable marker providing resistance to an antibiotic, such as a gene providing resistance to tetracycline. In the most preferred embodiment, the Fxe2x80x2 episome genetic material is derived from the Fxe2x80x2 episome of XL1-Blue.
The present invention also concerns processes for constructing E. coli bacteria containing Fxe2x80x2 genetic material capable of enhanced transformation efficiencies. In a preferred embodiment, the bacteria of the current invention is obtained by introducing Fxe2x80x2 genetic material into an E. coli bacterium. In a more preferred embodiment of the present invention, the bacterium of the present invention is obtained by mating E. coli XL1-Blue and E. coli DH5xcex1 bacteria. In an even more preferred embodiment of the present invention, the bacteria of the present invention is obtained by mating E. coli XL1-Blue and E. coli DH5xcex1/pCM301xcex94 bacteria (Tucker et al. Cell 36: 191-201 (1984)).